Nuno A. Fonseca

发表

A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

Mary Goldman, Junjun Zhang, Nuno A. Fonseca, 2019 .

Expression Atlas: gene and protein expression across multiple studies and organisms

Nuno A. Fonseca, Wojciech Bazant, Elisabet Barrera, 2017, Nucleic Acids Res..

LogCHEM: Interactive Discriminative Mining of Chemical Structure

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2008, 2008 IEEE International Conference on Bioinformatics and Biomedicine.

Moving Liposome Technology from the Bench to the Oncological Patient: Towards Performance-by-Design

Nuno A. Fonseca, Ana Filipa Cruz, Ana C. Gregório, 2018 .

Improving the performance of Transposable Elements detection tools

Nuno A. Fonseca, Rui Camacho, Jorge Vieira, 2013, J. Integr. Bioinform..

Predicting Malignancy from Mammography Findings and Surgical Biopsies

Nuno A. Fonseca, Elizabeth S. Burnside, Inês de Castro Dutra, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

A pipelined data-parallel algorithm for ILP

Nuno A. Fonseca, Rui Camacho, Fernando M. A. Silva, 2005, 2005 IEEE International Conference on Cluster Computing.

Studying the Relevance of Breast Imaging Features

Nuno A. Fonseca, Elizabeth S. Burnside, Inês de Castro Dutra, 2011, HEALTHINF.

Efficient and Scalable Induction of Logic Programs Using a Deductive Database System

Nuno A. Fonseca, Ricardo Rocha, Michel Ferreira, 2007, ILP.

iRAP - an integrated RNA-seq Analysis Pipeline

Nuno A. Fonseca, Robert Petryszak, John C. Marioni, 2014, bioRxiv.

Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2016, Resource Management for Big Data Platforms.

Tools for mapping high-throughput sequencing data

Nuno A. Fonseca, John C. Marioni, Alvis Brazma, 2012, Bioinform..

Gramene 2016: comparative plant genomics and pathway resources

Lincoln Stein, Nuno A. Fonseca, Robert Petryszak, 2015, Nucleic Acids Res..

BIORED - A Genetic Algorithm for Pattern Detection in Biosequences

Nuno A. Fonseca, Fernando M. A. Silva, Pedro Pereira Rodrigues, 2008, IWPACBB.

QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq

Nuno A. Fonseca, Rui Camacho, Luísa Pereira, 2017, PACBB.

Improving the efficiency of inductive logic programming systems

Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, 2009 .

Visually Guiding and Controlling the Search While Mining Chemical Structures

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2009, IWANN.

ADOPS - Automatic Detection Of Positively Selected Sites

Nuno A. Fonseca, Florentino Fernández Riverola, Miguel Reboiro-Jato, 2012, J. Integr. Bioinform..

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Jun Yu, Chen Hong, Ken Chen, 2020, Nature.

April - An Inductive Logic Programming System

Nuno A. Fonseca, Rui Camacho, Fernando M. A. Silva, 2006, JELIA.

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Nuno A. Fonseca, Robert Petryszak, Maria Keays, 2013, Nucleic Acids Res..

Compile the Hypothesis Space: Do it Once, Use it Often

Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, 2008, Fundam. Informaticae.

Gramene 2018: unifying comparative genomics and pathway resources for plant research

Bo Wang, Lincoln Stein, Nuno A. Fonseca, 2017, Nucleic Acids Res..

Conceptual Clustering of Multi-Relational Data

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2011, ILP.

Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2009, BSB.

Butler enables rapid cloud-based analysis of thousands of human genomes

Robert L. Grossman, Oliver Hofmann, Roland Eils, 2020, Nature Biotechnology.

Strategies to Parallelize ILP Systems

Nuno A. Fonseca, Rui Camacho, Fernando M. A. Silva, 2005, ILP.

VisAll: A Universal Tool to Visualise Parallel Execution of Logic Programs

Nuno A. Fonseca, Vítor Santos Costa, Inês de Castro Dutra, 1998, IJCSLP.

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Nuno A. Fonseca, Elisabet Barrera, Robert Petryszak, 2015, Nucleic Acids Res..

ArrayExpress update – from bulk to single-cell expression data

Nuno A. Fonseca, Robert Petryszak, Anja Füllgrabe, 2018, Nucleic Acids Res..

On Applying Tabling to Inductive Logic Programming

Nuno A. Fonseca, Ricardo Rocha, Vítor Santos Costa, 2005, ECML.

ILP : - Just Trie It

Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, 2007, ILP.

ILP: Compute Once, Reuse Often

Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, 2007 .

Online resources for PCAWG data exploration, visualization, and discovery

Mary Goldman, Junjun Zhang, Nuno A. Fonseca, 2017 .

Predicting the secondary structure of proteins using machine learning algorithms

Nuno A. Fonseca, Rui Camacho, Vânia Guimarães, 2012, Int. J. Data Min. Bioinform..

Assessing the Effect of 2D Fingerprint Filtering on ILP-Based Structure-Activity Relationships Toxicity Studies in Drug Design

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2011, PACBB.

Parallel ILP for distributed-memory architectures

Ashwin Srinivasan, Nuno A. Fonseca, Rui Camacho, 2009, Machine Learning.

Partitional Clustering of Protein Sequences - An Inductive Logic Programming Approach

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2009, IWANN.

Predicting malignancy from mammography findings and image-guided core biopsies

Nuno A. Fonseca, Elizabeth S. Burnside, Inês de Castro Dutra, 2015, Int. J. Data Min. Bioinform..

Boosting the Detection of Transposable Elements Using Machine Learning

Nuno A. Fonseca, Rui Camacho, Jorge Vieira, 2013, PACBB.

AND Parallelism for ILP: The APIS System

Nuno A. Fonseca, Rui Camacho, Ruy Ramos, 2013, ILP.

A Relational Learning Approach to Structure-Activity Relationships in Drug Design Toxicity Studies

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2011, J. Integr. Bioinform..

Induction as a search procedure

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2008 .

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data

Nuno A. Fonseca, Robert Petryszak, Anja Füllgrabe, 2017, Bioinform..

k-RNN: k-relational nearest neighbour algorithm

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2008, SAC '08.

Predicting the Start of Protein alpha-Helices Using Machine Learning Algorithms

Nuno A. Fonseca, Rui Camacho, Vânia Guimarães, 2010, IWPACBB.

A parallel ILP algorithm that incorporates incremental batch learning

Nuno A. Fonseca, Rui Camacho, Fernado Silva, 2003 .

Improving the efficiency of inductive logic programming systems

Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, 2009, Softw. Pract. Exp..

On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites

Nuno A. Fonseca, Florentino Fernández Riverola, Miguel Reboiro-Jato, 2012, PACBB.

Interactive Discriminative Mining of Chemical Fragments

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2010, ILP.

On Avoiding Redundancy in Inductive Logic Programming

Nuno A. Fonseca, Rui Camacho, Fernando M. A. Silva, 2004, ILP.

Experimental evaluation of a caching technique

Nuno A. Fonseca, Rui Camacho, Vítor Santos Costa, 2003 .

Efficient Data Structures for Inductive Logic Programming

Nuno A. Fonseca, Rui Camacho, Ricardo Rocha, 2003, ILP.

Experimental Evaluation of a Caching Technique for ILP

Nuno A. Fonseca, Rui Camacho, Fernando M. A. Silva, 2003, EPIA.

A Study on Burrows-Wheeler Aligner's Performance Optimization for Ancient DNA Mapping

Nuno A. Fonseca, Cindy Sarmento, Sílvia Guimarães, 2021, PACBB.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Nuno A. Fonseca, Shaun D. Jackman, David R. Kelley, 2011, Genome research.

Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.

Nuno A. Fonseca, Miguel Pignatelli, Julio Saez-Rodriguez, 2018, Cancer research.

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

Gunnar Rätsch, Nuno A. Fonseca, André Kahles, 2019, Cell.

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

Nuno A. Fonseca, Bianca M. Schmitt, D. Odom, 2014, Genome research.

Pan-cancer analysis of whole genomes

Steven J. M. Jones, Nuno A. Fonseca, Icgc, 2020, Nature.

Two independent modes of chromatin organization revealed by cohesin removal

Nuno A. Fonseca, L. Mirny, W. Huber, 2017, Nature.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Nuno A. Fonseca, Jonathan M. Mudge, J. Harrow, 2015, BMC Genomics.

Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

Nuno A. Fonseca, P. Beja, Bastian Egeter, 2020, bioRxiv.

Expression Atlas update: from tissues to single cells

Nuno A. Fonseca, Robert Petryszak, Irene Papatheodorou, 2019, Nucleic Acids Res..

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

Gunnar Rätsch, Junjun Zhang, Nuno A. Fonseca, 2017 .

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Lucas Lochovsky, Donghoon Lee, Chris Sander, 2017, bioRxiv.

Two independent modes of chromosome organization are revealed by cohesin removal

Nuno A. Fonseca, L. Mirny, W. Huber, 2016, bioRxiv.

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Nuno A. Fonseca, John C. Marioni, Alvis Brazma, 2014, bioRxiv.

An S-RNase-Based Gametophytic Self-Incompatibility System Evolved Only Once in Eudicots

Nuno A. Fonseca, Cristina P. Vieira, Jorge Vieira, 2008, Journal of Molecular Evolution.

Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer

Nuno A. Fonseca, Alvis Brazma, Liliana Greger, 2017, bioRxiv.

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Nuno A. Fonseca, Alvis Brazma, John Marioni, 2014, bioRxiv.

An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile

Nuno A. Fonseca, D. Glez-Peña, H. López-Fernández, 2020, Frontiers in Immunology.

Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study

Nuno A. Fonseca, D. Bishop, A. Brazma, 2020, bioRxiv.

A user guide for the online exploration and visualization of PCAWG data

Nuno A. Fonseca, Brian D. O’Connor, D. Haussler, 2020, Nature Communications.

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Convergent Evolution at the Gametophytic Self-Incompatibility System in Malus and Prunus

Nuno A. Fonseca, J. Vieira, C. Vieira, 2015, PloS one.

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

Wan Choi, Oliver Hofmann, Roland Eils, 2017, bioRxiv.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

Nuno A. Fonseca, A. Brazma, C. Creighton, 2017, bioRxiv.

Integrative pathway enrichment analysis of multivariate omics data

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Pan-cancer study of heterogeneous RNA aberrations

Nuno A. Fonseca, Angela N. Brooks, Stefan G. Stark, 2017, bioRxiv.

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Communications Biology.

Pathway and network analysis of more than 2500 whole cancer genomes

Nuno A. Fonseca, Icgc, Gary D Bader, 2020, Nature Communications.

Improving the performance of Transposable Elements detection tools

Nuno A. Fonseca, Rui Camacho, J. Vieira, 2013, Journal of integrative bioinformatics.

Transcription factor activities enhance markers of drug response in cancer

Nuno A. Fonseca, G. Bignell, F. Iorio, 2017, bioRxiv.

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

Nuno A. Fonseca, Angela N. Brooks, David T. W. Jones, 2020, Nature Communications.

Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model

Nuno A. Fonseca, David Reboiro-Jato, M. Reboiro-Jato, 2013, Journal of experimental botany.

Tumors induce de novo steroid biosynthesis in T cells to evade immunity

Nuno A. Fonseca, Lia S. Campos, S. Teichmann, 2018, Nature Communications.

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system

Nuno A. Fonseca, J. Vieira, C. Vieira, 2018, Scientific Reports.

ADOPS - Automatic Detection Of Positively Selected Sites

Nuno A. Fonseca, David Reboiro-Jato, M. Reboiro-Jato, 2012, Journal of integrative bioinformatics.

The Drosophila melanogaster methuselah Gene: A Novel Gene with Ancient Functions

Nuno A. Fonseca, David Reboiro-Jato, M. Reboiro-Jato, 2013, PloS one.

Drosophila americana as a Model Species for Comparative Studies on the Molecular Basis of Phenotypic Variation

Nuno A. Fonseca, C. Schlötterer, J. Vieira, 2013, Genome biology and evolution.

The number, age, sharing and relatedness of S-locus specificities in Prunus.

Nuno A. Fonseca, J. Vieira, C. Vieira, 2008, Genetics research.

Complete Genome Sequence Obtained by Nanopore and Illumina Hybrid Assembly of Xanthomonas arboricola pv. juglandis CPBF 427, Isolated from Buds of a Walnut Tree

Nuno A. Fonseca, Miguel C. Teixeira, C. Chaves, 2021, Microbiology Resource Announcements.

Protein evolution of ANTP and PRD homeobox genes

Nuno A. Fonseca, P. Holland, J. Vieira, 2008, BMC Evolutionary Biology.

Genomic basis for RNA alterations in cancer

Mary Goldman, Nuno A. Fonseca, Brian Craft, 2020, Nature.

Patterns of somatic structural variation in human cancer genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

the molecular basis of phenotypic variation

Nuno A. Fonseca, C. Schlötterer, J. Vieira, 2013 .

The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions

Nuno A. Fonseca, C. Schlötterer, J. Vieira, 2012, Fly.

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Nuno A. Fonseca, J. Marioni, F. Spitz, 2014, Nature Genetics.

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Integrative pathway enrichment analysis of multivariate omics data

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2018, bioRxiv.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Inanç Birol, Dominique Lavenier, Hamidreza Chitsaz, 2013, GigaScience.

Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

Nuno A. Fonseca, A. Brazma, C. Creighton, 2022, Nature communications.

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system

Nuno A. Fonseca, J. Vieira, C. Vieira, 2018, Scientific Reports.

Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree

Nuno A. Fonseca, Miguel C. Teixeira, J. Blom, 2021, Microorganisms.

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

Nuno A. Fonseca, G. Rätsch, A. Brazma, 2018 .

Phylogeny of the teashirt‐related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafish

Nuno A. Fonseca, J. Vieira, C. Vieira, 2010, Developmental dynamics : an official publication of the American Association of Anatomists.

Author Correction: Integrative pathway enrichment analysis of multivariate omics data

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

Comprehensive molecular characterization of mitochondrial genomes in human cancers

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2017, bioRxiv.

Author Correction: Pan-cancer analysis of whole genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2023, Nature.

Sex differences in oncogenic mutational processes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2019, Nature Communications.

A user guide for the online exploration and visualization of PCAWG data

Nuno A. Fonseca, Brian D. O’Connor, D. Haussler, 2020, Nature Communications.

Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus)

Nuno A. Fonseca, Pedro G. Ferreira, J. Vieira, 2010, BMC Evolutionary Biology.

RNase-Based Gametophytic Self-Incompatibility Evolution: Questioning the Hypothesis of Multiple Independent Recruitments of the S-Pollen Gene

Nuno A. Fonseca, J. Vieira, C. Vieira, 2009, Journal of Molecular Evolution.

The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera

Nuno A. Fonseca, P. Beja, L. Quaglietta, 2020, Biodiversity data journal.

The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01

Nuno A. Fonseca, P. Beja, J. Paupério, 2020, Biodiversity data journal.

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Nuno A. Fonseca, Benjamin J. Raphael, Allison P. Heath, 2020, Nature Communications.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

Apr 27, 2021 Pathway and network analysis of more than 2500

Nuno A. Fonseca, Gary D Bader, Calvin Wing Yiu Chan, 2020 .

Open Access Research Article Evolutionary Patterns at the Rnase Based Gametophytic Self -incompatibility System in Two Divergent Rosaceae Groups (maloideae and Prunus)

Nuno A. Fonseca, Pedro G. Ferreira, J. Vieira, 2022 .

Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case

Nuno A. Fonseca, J. Vieira, C. Vieira, 2009, PloS one.

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Nuno A. Fonseca, J. Marioni, A. Brazma, 2014, bioRxiv.

Transcription factor activities enhance markers of drug response in cancer

Nuno A. Fonseca, G. Bignell, F. Iorio, 2017, bioRxiv.

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Nuno A. Fonseca, J. Marioni, F. Spitz, 2014, Nature Genetics.

A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations

Nuno A. Fonseca, Angela N. Brooks, G. Rätsch, 2017, bioRxiv.

Tumour gene expression signature in primary melanoma predicts long-term outcomes

Nuno A. Fonseca, D. Bishop, A. Brazma, 2021, Nature Communications.

Analyses of non-coding somatic drivers in , cancer whole genomes

Nuno A. Fonseca, Kahraman, Todd A. Johnson, 2020 .